Contacts of the strand formed by residues 71 - 76 (chain B) in PDB entry 2QXU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASN* 4.0 0.9 - - - -
5B PRO* 3.4 13.9 - - + +
7B VAL* 4.0 16.6 - - + -
59B VAL* 3.8 20.4 - - + -
62B VAL* 3.9 24.9 - - + -
63B LEU* 3.5 26.2 - - + -
70B LYS* 1.3 75.0 - - - +
72B ASP* 1.3 68.2 + - - +
73B ILE* 4.3 11.4 - - + -
95B LYS 2.9 17.2 + - - +
96B VAL* 3.3 7.8 - - + +
97B ALA 3.0 23.4 + - - -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B HIS* 5.6 0.5 - - - -
4B ASN* 3.2 37.9 + - - +
5B PRO 3.0 10.2 + - - +
6B VAL* 3.4 9.6 - - + +
7B VAL* 2.9 25.5 + - - +
31B TRP* 5.5 1.9 + - - -
71B VAL* 1.3 73.5 - - - +
73B ILE* 1.3 63.1 + - - +
97B ALA* 3.3 1.9 - - - +
98B ASN* 2.9 49.0 + - - +
173B LEU* 3.5 29.4 - - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 3.2 19.1 - - + +
9B VAL* 3.8 11.7 - - + -
55B LEU* 4.9 5.2 - - + -
59B VAL* 4.9 5.4 - - + -
71B VAL* 4.3 7.0 - - + -
72B ASP* 1.3 80.6 - - - +
74B VAL* 1.3 74.1 + - - +
75B ALA* 4.1 2.9 - - + +
83B THR* 3.7 43.7 - - + +
86B TYR* 4.5 13.7 - - + -
96B VAL* 4.0 27.8 - - + -
98B ASN 2.9 13.0 + - - +
99B VAL* 3.5 7.7 - - + -
100B VAL* 2.9 26.3 + - - +
173B LEU* 4.6 2.0 - - - +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.9 19.1 - - + -
7B VAL 3.1 5.9 + - - -
8B MET* 3.2 15.1 - - + +
9B VAL 2.8 22.5 + - - -
19B PHE* 3.9 12.3 - - + -
22B ILE* 4.5 7.6 - - + -
73B ILE* 1.3 79.0 - - - +
75B ALA* 1.3 60.1 + - - +
100B VAL* 3.2 11.9 - - + +
102B LEU* 4.0 26.2 - - + -
169B ILE* 4.1 26.5 - - + -
173B LEU* 4.0 15.9 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.3 9.6 - - + +
19B PHE* 4.8 0.7 - - - -
73B ILE* 4.0 4.0 - - + -
74B VAL* 1.3 75.4 - - - +
76B HIS* 1.3 57.0 + - - +
79B GLY 3.5 29.4 - - - +
80B GLY* 3.7 7.6 - - - +
83B THR* 3.6 14.4 - - - +
100B VAL 2.8 11.9 + - - +
101B THR* 3.2 8.3 - - + -
102B LEU* 2.7 35.5 + - - +
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL 2.9 12.0 + - - +
10B HIS* 4.8 0.4 - - - -
11B GLY* 3.3 19.8 + - - +
18B ASN* 5.6 3.4 + - - -
19B PHE* 4.1 7.6 - - + -
75B ALA* 1.3 73.4 - - - +
77B SER* 1.3 69.7 + - - +
78B MET 3.2 0.2 + - - -
79B GLY* 2.8 20.9 + - - -
102B LEU* 3.4 28.9 - - + -
156B HIS* 3.0 54.5 + + - -
157B ILE* 4.8 3.6 - - + -
159B LEU* 4.3 3.6 - - + +
160B LEU* 4.0 43.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il